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Genetics > Chapter 14 > Flashcards

Chapter 14 Flashcards

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1
Q

what is a gene?

A

a gene is unit of hereditary information that occupies a fixed position (locus) on a chromosome

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2
Q

what is the central dogma?

A

proposed by Francis Crick in the late 1950s. This trailblazing theory suggested that genetic information flows primarily from nucleic acids in the form of DNA and RNA to functional proteins during the process of gene expression

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3
Q

what is gene expression?

A

the process by which the information encoded in a gene is used to direct the synthesis of a functional gene product, typically a protein

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4
Q

what makes up a transcriptional unit?

A

Promoter → Transcription Start Site → Coding Sequence (with potential introns/exons) → Terminator

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5
Q

what are the parts of DNA that are important in transcription?

A

the promoter region (with its core and proximal elements), transcription start site, coding region, terminator sequence, and various regulatory elements such as enhancers and silencers.

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6
Q

what are the parts of an mRNA that are transcribed?

A

The initial transcript (pre-mRNA) includes the 5’ UTR, coding sequence (exons and introns), and 3’ UTR. After processing, mature mRNA consists of a 5’ cap, 5’ UTR, exons (coding sequence), 3’ UTR, and poly-A tail

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7
Q

what is transcription?

A

process of taking DNA turning it into RNA

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8
Q

What are the specific things needed for transcription to take place?

A

DNA template strand with a promoter region.
RNA polymerase enzyme.
General and specific transcription factors (in eukaryotes).
Ribonucleotides (NTPs).
Enhancer and silencer elements (for regulation).
Transcription start site (TSS).
Helicase activity to unwind the DNA.
Energy supply (ATP and other NTPs).
Regulatory proteins and, in eukaryotes, cofactors and mediator complexes.

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9
Q

what is the difference between the template strand and the coding strand of DNA?

A

The template strand is read by RNA polymerase to synthesize RNA and runs 3’ to 5’.
The coding strand matches the RNA transcript’s sequence (with T replaced by U) and runs 5’ to 3’.
The template strand is complementary to both the RNA and the coding strand, while the coding strand is the non-template strand with the same sequence as the RNA

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10
Q

what are the 3 parts of a transcriptional unit?

A

Promoter: Initiates transcription.
Structural gene: Contains the RNA-coding sequence.
Terminator: Marks the end of transcription

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11
Q

What are the steps involved in transcription?

A

Initiation
Elongation
Termination

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12
Q

What is the promoter?

A

a sequence within a gene that initiates transcription

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13
Q

Where is the promoter located?

A

On DNA near 5’ end, located within the TSS (transcription start site)

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14
Q

What does RNA polymerase do?

A

synthesizes the strand of RNA using a DNA template

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15
Q

does RNA polymerase proofread as the nucleotides are added?

A

RNA polymerase has a very limited ability to proofread compared to DNA polymerase. It does possess a rudimentary form of proofreading, where it can backtrack, remove incorrectly incorporated nucleotides, and then resume synthesis. However, this mechanism is much less efficient than the proofreading by DNA polymerase

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16
Q

Does RNA polymerase need a primer?

A

unlike DNA polymerase, RNA polymerase does not require a primer to initiate transcription

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17
Q

How does RNA polymerase know where to go?

A

RNA polymerase knows where to go by recognizing promoter regions on the DNA, assisted by transcription factors in eukaryotes or the sigma factor in prokaryotes

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18
Q

What is the sigma factor

A

transcription factor that recognizes bacterial promoter sequences and facilitates the binding of RNA polymerase to the promoter

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19
Q

What direction is RNA made?

A

5’ to 3’

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20
Q

what is meant by DNA is described as an open complex? closed?

A

“open complex” means that the double-stranded DNA has been partially unwound to form a transcription bubble, allowing RNA polymerase access to the template strand for RNA synthesis
“closed complex” describes the state where RNA polymerase has bound to the promoter region of DNA, but the DNA strands are still intact and double-stranded

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21
Q

what is a terminator?

A

sequence within a gene that signals the end of transcription

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22
Q

what are the 2 major types of terminators in bacteria?

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A

p-independent or p-dependent

23
Q

How are the two terminators in bacteria alike?

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A

Purpose: Both types serve to terminate transcription and release the RNA transcript.
DNA Sequence Involvement: Both are triggered by specific DNA sequences that lead to termination.
Mechanism Outcome: Both result in RNA polymerase stopping transcription and detaching from the DNA.

24
Q

how are the two types of terminators in bacteria different?

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A

Intrinsic (rho independent) terminators rely on RNA structures (e.g., hairpin loops) to terminate transcription.
Rho-dependent terminators require the rho protein, which moves along the RNA to catch up with RNA polymerase and induce termination when it pauses at a specific site.

25
how does bacterial RNA polymerase compare to eukaryotic RNA polymerase?
Number of Types: Bacteria: Typically have one RNA polymerase that transcribes all types of RNA (mRNA, tRNA, and rRNA). Eukaryotes: Have three main RNA polymerases (RNA polymerase I, II, and III), each specialized for transcribing different types of genes. Structure: Bacterial RNA Polymerase: Composed of a simpler core enzyme structure, often made up of four main subunits (α, β, β', and ω) and a sigma factor that aids in promoter recognition. Eukaryotic RNA Polymerases: More complex, with each polymerase consisting of 12 or more subunits and requiring a suite of general transcription factors to initiate transcription. Promoter Recognition: Bacteria: Use a sigma factor that associates with the core RNA polymerase to recognize specific promoter sequences and initiate transcription. Eukaryotes: Utilize a variety of general transcription factors (e.g., TFIID, TFIIB, TFIIH) to assist in the binding of RNA polymerase to promoter regions.
26
what do the different eukaryotic RNA polymerases transcribe?
RNA Polymerase I: Transcribes: Ribosomal RNA (rRNA), specifically the large rRNA precursors (28S, 18S, and 5.8S rRNA). RNA Polymerase II: Transcribes: Messenger RNA (mRNA), small nuclear RNAs (snRNAs), and some small nucleolar RNAs (snoRNAs). RNA Polymerase III: Transcribes: Transfer RNA (tRNA), 5S rRNA, and other small RNAs, including U6 snRNA and some regulatory RNAs.
27
what are the differences between transcription in bacteria and eukaryotes?
Bacterial transcription is simpler, occurs in the cytoplasm, and often couples with translation. It involves a single RNA polymerase, minimal RNA processing, and simpler regulation. Eukaryotic transcription is more complex, occurs in the nucleus, involves three RNA polymerases, requires significant RNA processing (capping, splicing, and polyadenylation), and has intricate regulation involving various transcription factors and chromatin remodeling.
28
what do general transcription factors do?
one of several proteins that are necessary for a basal level of transcription at the core promoter in eukaryotes
29
what is a mediator?
a protein complex that interacts with RNA polymerase II, can stimulate or inhibit it
30
what does it mean to be colinear?
the direct correspondence between the sequence of nucleotides in DNA (or RNA) and the sequence of amino acids in a protein. This means that the linear sequence of codons in mRNA (transcribed from DNA) maps directly to the linear sequence of amino acids in a protein, maintaining the same order
31
what does it mean to be not colinear?
means that the linear sequence of nucleotides in the DNA does not correspond directly to the linear sequence of amino acids in the resulting protein. This lack of colinearity indicates that the initial RNA transcript or DNA contains non-coding regions (introns) or other elements that interrupt the sequence that will be translated into protein
32
what is an intron?
intervening sequences that are found between exons, they are spiced out of the RNA prior to translation
33
what is an exon?
segment contained within the RNA after splicing has occurred
34
How are introns and exons positioned relative to each other on mRNA?
Exons: These are the coding sequences that remain in the mature mRNA after splicing and are translated into proteins. Introns: These non-coding sequences are located between the exons in the pre-mRNA and are removed during RNA processing. Final mRNA: Contains only the exons, arranged in their original order, flanked by the 5' UTR and 3' UTR for regulatory purposes.
35
What is the basic structure of an mRNA molecule?
5' Cap → 5' UTR → Start Codon → Coding Sequence (CDS) → Stop Codon → 3' UTR → Poly-A Tail
36
what are some post-transcriptional modifications that occur to eukaryotic mRNA?
5' Capping: Addition of a 5' cap for stability, protection, and translation initiation. 3' Polyadenylation: Addition of a poly-A tail for stability and export. RNA Splicing: Removal of introns and joining of exons to form a continuous coding sequence. RNA Editing: Alteration of the nucleotide sequence in some cases. RNA Transport and Localization: Processes ensuring that mature mRNA is transported from the nucleus to the cytoplasm.
37
How and where are rRNA processed?
Where: nucleus how: Transcription: rRNA genes are transcribed by RNA polymerase I (for 28S, 18S, and 5.8S rRNA) and RNA polymerase III (for 5S rRNA). Cleavage: The primary transcript, known as 45S pre-rRNA in eukaryotes, undergoes several cleavage steps to produce the mature rRNA components (28S, 18S, and 5.8S rRNA). These cleavages are facilitated by a complex set of nucleases. Chemical Modifications: Methylation: Certain nucleotides are methylated. Pseudouridylation: Some uridines are converted to pseudouridines. Assembly: The processed rRNA is assembled with ribosomal proteins to form the small (40S) and large (60S) ribosomal subunits, which are then transported to the cytoplasm to participate in translation.
38
How and where are tRNA processed?
where: nucleus, with some final modifications occurring in the cytoplasm how: Transcription: tRNA genes are transcribed by RNA polymerase III to produce a primary tRNA transcript. Cleavage: The 5' leader sequence is removed by RNase P, an enzyme with both RNA and protein components. The 3' trailer sequence is trimmed by various endonucleases and exonucleases. Addition of CCA Sequence: The CCA sequence is added to the 3' end if it is not encoded in the gene. This step is crucial for tRNA function, as it is where the amino acid attaches. Splicing (for some tRNAs): In eukaryotic tRNAs that have introns, these introns are removed by specialized tRNA splicing enzymes. Chemical Modifications: tRNAs undergo various modifications, such as the methylation of bases and conversion of uridines to pseudouridines, to ensure correct folding and functionality. Folding: The tRNA folds into its characteristic cloverleaf structure, which is essential for its role in translation. Export to the Cytoplasm: Once processing is complete, mature tRNA is exported from the nucleus to the cytoplasm by specific transport proteins.
39
what is the difference between the Group 1 and Group 2 splicing and the spliceosome?
Group I and II splicing are self-splicing mechanisms where the RNA itself catalyzes the removal of introns, with Group I using a guanosine cofactor and Group II forming a lariat structure. Spliceosome-mediated splicing is the standard mechanism in eukaryotic nuclear mRNA processing and involves a complex of snRNPs and proteins that facilitate the splicing process and require ATP for its function. The spliceosome closely resembles Group II intron splicing, suggesting an evolutionary link.
40
what is the significance of alternate splicing?
allows two or more different polypeptide sequences to be derived from a single gene, speculating that this allows an organism to carry fewer genes in its genome
41
What is the purpose of the 5' cap?
required for proper exit of most mRNA's from the nucleus, recognized as an initiation actor that causes the mRNA to bind to a ribosome during the initiation of translation, may be important in the efficient splicing of introns
42
do you find 5' cap in both prokaryotes and eukaryotes? is their function the same?
No, the 5' cap is found only in eukaryotic mRNA and not in prokaryotic mRNA
43
What is the purpose of polyA tail?
important for mRNA stability, the exit of mRNA from the nucleus, and synthesis of polypeptides
44
do you find poly a tail in both prokaryotes and eukaryotes? is their function the same?
Poly-A Tail Presence: Common in eukaryotes and an essential feature of most eukaryotic mRNAs. Occasional in prokaryotes, but with a different and less significant role. Function: Eukaryotic mRNA: The poly-A tail stabilizes the mRNA, assists in translation initiation, and aids in nuclear export. Prokaryotic mRNA: Polyadenylation typically promotes mRNA degradation rather than stability, serving as a mechanism for regulating mRNA turnover.
45
What are the key differences of a promoter in bacteria and eukaryotes?
B: consists of -35 and -10 sequences E: the core promoter often consists of a TATA box and a transcriptional start site
46
What are the key differences of a RNA polymerase in bacteria and eukaryotes?
B: single RNA polymerase E: 3 types of RNA polymerases, RNA polymerase II transcribes protein-coding genes
47
What are the key differences of a Initiation during transcription in bacteria and eukaryotes?
B: Sigma factor is needed for promoter recognition E: Five general transcription factors assemble at the core promoter
48
What are the key differences of a Elongation during transcription in bacteria and eukaryotes?
B: requires the release of sigma factor E: Mediator controls the switch to elongation phase
49
What are the key differences of a Termination during transcription in bacteria and eukaryotes?
B: is either rho-dependent or rho-independent E: According to the allosteric or torpedo model
50
What are the key differences of splicing in bacteria and eukaryotes?
B: very rare; self-splicing E: Commonly occurs in protein-coding pre-mRNAs in complex eukaryotes via a spliceosome; self-splicing occurs rarely
51
What are the key differences of capping in bacteria and eukaryotes?
B: does not occur E: addition of 7-methylguanosine cap
52
What are the key differences of tailing in bacteria and eukaryotes?
B: added to the 3' end; promotes degradation E: added to the 3' end; promotes stability
53

Genetics (8 decks)

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